Raw molecular dynamics (LAMMPS) dump files, X-ray diffraction (XRD) compute outputs, and text files containing velocity autocorrelation function (VACF) measurements, computed vibrational density of states (VDoS) profiles, and microstructural descriptors of the dump files. Data was collected using the molecular dynamics code LAMMPS from simulations of bulk silicon, gold, magnesium, and iron with and without disorder insertion and with and without mechanical loading. A portion of the Si data provided in this dataset was used for a previous publication (10.1021/acs.chemmater.2c03207).